Uploading your data

In the Data menu, you can directly drag and drop files or use the Browse files to select images. File upload happens in two stages:

1. File Selection and organization

You can add files for uploading by:

• Drag and drop files or folders
• Clicking Browse files and select files or folders
• You don't have to select all the files at once. You can drop or select additional files at this stage.

Files Selected for uploading show up with detected animal names, staining, magnification and AP coordinate. At this stage, nothing has been uploaded yet and your job is to verify that everything was detected correctly from the filenames, and correct any issues.

2. Uploading

Once you are happy with the detected and potentially manually corrected files, click Upload. All the selected files will now start uploading in sequence. Keep the page open until the upload is complete.

How metadata detection works

From each filename, Neuro QP tries to detect:

• Animal
• Staining (including aliases)
• Magnification (4x or 20x)
• AP coordinate

The way this works is that Neuro QP simply tries to check if any of your defined animal names is present in the filename, if any of your staining names or aliases for stainings is present, and checks if it finds AP followed by a number (positive or negative) in the filename.

Files selected for upload are grouped by animal and AP coordinates. For processing, we need complete slice data, so one slice should have DAPI at 20x and 4x, and all staining at 20x. See the Data requirements section for more information.

Remeber that detected values are matched against the Study setup you already configured.

Filename best practices

Use predictable filenames that include the key metadata parts. Keep naming consistent across your entire dataset.. This not only simplifies the uploading of data, but helps you organize your files for yourself as well.

Recommended structure:

• [Animal]_[Staining]_[Magnification]_AP[-n.nn].ext

Example filenames for a full slice with detected animals, stainings, magnification and AP coordinates:

Batch strategy

Instead of uploading hundreds of images at once, it's usually best to do the upload in multiple batches, for example all images for one animal at a time.

• Make sure your filenames have all the expected information in them, see Filename best practices above.
• Confirm warnings are resolved before starting large uploads.

Organize and validate before upload

In staging, review each slice group before clicking Upload. You might encounter the following warnings:

• Unknown animal: No animal was detected in the slice. Check the filename and if it matches an animal you defined in the Study Animals section.
• Staining not detected: No staining that is defined in the Study was not detected. Check the filename and potentially add an alias for the staining (example would be you only defined the staining NeuN, but the filename uses red for that staining).
• Magnification not detected: 20x or 4x was not detected in the filename.
• AP coordinate not detected: Neuro QP expects the format AP[n.nn], where n.nn is the coordinate like 0.23 or -1.23.
• Duplicate Filenames: You get this warning if the filename was already uploaded.

Critical warnings should be resolved first to avoid incomplete processing later.

Final upload

After clicking Upload, keep the tab open until upload completes.

• Files upload slice-by-slice,
• Upload can take time for larger batches and depends on your internet connection.
• Transient failures are retried a few times automatically.
• If retries fail, upload pauses and lets you retry or abort.

After upload succeeds, processing starts automatically (alignment, atlas registration, cell detection) when prerequisites are available. See What happens after upload for details.